Identifying orthologs and comparing gene structures in a pan-genome using whole genome multiple alignments. The input is provided as a set of genomic sequences (FASTA format) and gene annotations (GFF3 format). Whole genome multiple alignments (top left) are first calculated using Mugsy . Mugsy-Annotator then builds groups of orthologous gene structures that are conserved in sequence and genomic context according to the alignment. The alignment also indicates the location of each predicted translation initiation start and stop across the genomes, allowing for identification of annotation anomalies or missing annotations.